Introduction to R 2025
Faculty: Mohamed Helmy
October 6-7, 2025
I Introduction
1 Workshop Info
Welcome to the 2025 Introduction to R Canadian Bioinformatics Workshop webpage!
1.1 Pre-work
1.2 Class Photo
1.3 Schedule
2 Meet Your Faculty
2.0.0.1 Mohamed Helmy
Principal Scientist and Adjunct Professor
Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan
Saskatoon, Saskatchewan, Canada
Mohamed is a Computational Systems Biologist and Principal Scientist leading the Bioinformatics and Systems Biology Lab (BSBL) at the Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan. He received his MSc and PhD in Computational Systems Biology from Keio University (Tokyo, Japan) and completed his postdoctoral training in bioinformatics at Kyoto University and the University of Toronto. Mohamed’s interdisciplinary research profile bridges biology, computer science, and public health.
2.0.0.2 Sylvia Li
Graduate student
Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan
Saskatoon, Saskatchewan, Canada
Sylvia is a Computer science MSc student at the University of Saskatchewan, supervised by Dr. Helmy. She holds dual BSc degrees in Bioinformatics and Computer science. Currently her work focuses on bacterial genomic data.
Data and Compute Setup
2.0.0.3 Course data downloads
Coming soon!
2.0.0.4 Compute setup
Coming soon!
II Modules
3 Module 1
3.1 Lecture
3.1.1 1A
3.1.2 1B
3.2 Lab 1A
3.2.1 Variables
Create 2 numeric variables and assign values for each
x = 10
y = 6Calculate the sum of them
total = x + y
total## [1] 16Calculate the square root of the total
sr = sqrt(total)
sr## [1] 43.2.2 Data Structures
Vector
v <- c(1,2,3,4)
v## [1] 1 2 3 4Matrix
m <- matrix(1:6, nrow = 2)
m## [,1] [,2] [,3]
## [1,] 1 3 5
## [2,] 2 4 6Dataframe
df <- data.frame(age=c(25,30), name=c("Mo","Tom"), group=c("A", "B"))
df## age name group
## 1 25 Mo A
## 2 30 Tom BList
lst <- list(numbers=v, info=df)
lst## $numbers
## [1] 1 2 3 4
##
## $info
## age name group
## 1 25 Mo A
## 2 30 Tom B3.3 Lab 1B
3.3.1 Install BioconductoR packages
install.packages("BiocManager")
BiocManager::install("ALL")3.3.2 View patient metadata
library(BiocManager)
library(ALL)
data(ALL)
df2 <- pData(ALL)3.3.3 Quick summary
#summary(pData(ALL)[, c("age", "sex", "BT", "relapse")])
summary(df2[, c("age", "sex", "BT", "relapse")])## age sex BT relapse
## Min. : 5.00 F :42 B2 :36 Mode :logical
## 1st Qu.:19.00 M :83 B3 :23 FALSE:35
## Median :29.00 NA's: 3 B1 :19 TRUE :65
## Mean :32.37 T2 :15 NA's :28
## 3rd Qu.:45.50 B4 :12
## Max. :58.00 T3 :10
## NA's :5 (Other):133.3.4 str() and dim() functions
dim(df2)## [1] 128 21str(df2)## 'data.frame': 128 obs. of 21 variables:
## $ cod : chr "1005" "1010" "3002" "4006" ...
## $ diagnosis : chr "5/21/1997" "3/29/2000" "6/24/1998" "7/17/1997" ...
## $ sex : Factor w/ 2 levels "F","M": 2 2 1 2 2 2 1 2 2 2 ...
## $ age : int 53 19 52 38 57 17 18 16 15 40 ...
## $ BT : Factor w/ 10 levels "B","B1","B2",..: 3 3 5 2 3 2 2 2 3 3 ...
## $ remission : Factor w/ 2 levels "CR","REF": 1 1 1 1 1 1 1 1 1 1 ...
## $ CR : chr "CR" "CR" "CR" "CR" ...
## $ date.cr : chr "8/6/1997" "6/27/2000" "8/17/1998" "9/8/1997" ...
## $ t(4;11) : logi FALSE FALSE NA TRUE FALSE FALSE ...
## $ t(9;22) : logi TRUE FALSE NA FALSE FALSE FALSE ...
## $ cyto.normal : logi FALSE FALSE NA FALSE FALSE FALSE ...
## $ citog : chr "t(9;22)" "simple alt." NA "t(4;11)" ...
## $ mol.biol : Factor w/ 6 levels "ALL1/AF4","BCR/ABL",..: 2 4 2 1 4 4 4 4 4 2 ...
## $ fusion protein: Factor w/ 3 levels "p190","p190/p210",..: 3 NA 1 NA NA NA NA NA NA 1 ...
## $ mdr : Factor w/ 2 levels "NEG","POS": 1 2 1 1 1 1 2 1 1 1 ...
## $ kinet : Factor w/ 2 levels "dyploid","hyperd.": 1 1 1 1 1 2 2 1 1 NA ...
## $ ccr : logi FALSE FALSE FALSE FALSE FALSE FALSE ...
## $ relapse : logi FALSE TRUE TRUE TRUE TRUE TRUE ...
## $ transplant : logi TRUE FALSE FALSE FALSE FALSE FALSE ...
## $ f.u : chr "BMT / DEATH IN CR" "REL" "REL" "REL" ...
## $ date last seen: chr NA "8/28/2000" "10/15/1999" "1/23/1998" ...3.3.5 the table() function
af <- table(df2$age)
barplot(af, main = "Age frec.")
### mean and median age
mn <- mean(df2$age) # this will return NA
md <- median(df2$age) # this will return NA
mn <- mean(df2$age, na.rm = TRUE) # this will work
md <- median(df2$age, na.rm = TRUE) # this will work3.3.6 standard deviation and variance
std <- sd(df2$age, na.rm = TRUE)
vr <- var(df2$age, na.rm = TRUE)3.3.7 Extremes
mxx <- max(df2$age, na.rm = T)
mnn <- min(df2$age, na.rm = T)3.3.8 Table and (Frequency)
age_dit <- table(df2$age)3.3.9 Quick summary
summary(df2[, c("age", "sex", "BT", "relapse")])## age sex BT relapse
## Min. : 5.00 F :42 B2 :36 Mode :logical
## 1st Qu.:19.00 M :83 B3 :23 FALSE:35
## Median :29.00 NA's: 3 B1 :19 TRUE :65
## Mean :32.37 T2 :15 NA's :28
## 3rd Qu.:45.50 B4 :12
## Max. :58.00 T3 :10
## NA's :5 (Other):133.3.10 Patients older than 40
older_patients <- subset(df2, age > 40)3.3.11 Patients who relapsed
relapsed_patients <- subset(df2, relapse == TRUE)3.3.12 Subsetting and Filtering
3.3.12.1 subset()
subset(df2, age > 40 & relapse == TRUE)## cod diagnosis sex age BT remission CR date.cr t(4;11) t(9;22)
## 03002 3002 6/24/1998 F 52 B4 CR CR 8/17/1998 NA NA
## 04007 4007 7/22/1997 M 57 B2 CR CR 9/17/1997 FALSE FALSE
## 08012 8012 10/22/1998 M 55 B3 CR CR 1/9/1999 FALSE FALSE
## 15004 15004 2/10/2000 M 44 B1 CR CR 4/3/2000 TRUE FALSE
## 16004 16004 4/19/1997 F 58 B1 CR CR 7/15/1997 TRUE FALSE
## 19005 19005 11/15/1997 F 48 B1 CR CR 2/3/1998 FALSE FALSE
## 20002 20002 5/9/1997 F 58 B2 CR CR 8/19/1997 FALSE TRUE
## 24005 24005 1/3/1997 F 45 B1 CR CR 4/8/1997 TRUE FALSE
## 24017 24017 9/15/1998 M 57 B2 CR CR 12/7/1998 FALSE TRUE
## 26003 26003 2/18/1998 F 49 B4 CR CR 4/21/1998 FALSE FALSE
## 28028 28028 7/8/1998 M 47 B1 CR CR 9/3/1998 TRUE FALSE
## 28036 28036 12/23/1998 M 52 B3 CR CR 3/8/1999 FALSE TRUE
## 43001 43001 11/14/1996 M 41 B1 CR CR 1/30/1997 FALSE TRUE
## 49006 49006 8/12/1998 F 43 B2 CR CR 11/19/1998 NA NA
## 62003 62003 12/4/1998 M 53 B4 CR CR 1/28/1999 FALSE TRUE
## 63001 63001 7/8/1997 M 49 B1 CR CR 9/2/1997 NA NA
## 84004 84004 9/25/1998 M 50 B CR CR 12/1/1998 NA NA
## 16002 16002 4/10/1997 M 50 T3 CR CR 6/10/1997 NA NA
## 43015 43015 2/29/2000 M 52 T2 CR CR 6/8/2000 FALSE FALSE
## cyto.normal citog mol.biol fusion protein mdr kinet ccr
## 03002 NA <NA> BCR/ABL p190 NEG dyploid FALSE
## 04007 FALSE del(6q) NEG <NA> NEG dyploid FALSE
## 08012 FALSE simple alt. NEG <NA> NEG dyploid FALSE
## 15004 FALSE t(4;11) ALL1/AF4 <NA> NEG dyploid FALSE
## 16004 FALSE t(4;11) ALL1/AF4 <NA> NEG dyploid FALSE
## 19005 TRUE normal ALL1/AF4 <NA> NEG dyploid FALSE
## 20002 FALSE t(9;22)+other BCR/ABL p190 NEG dyploid FALSE
## 24005 FALSE t(4;11) ALL1/AF4 <NA> NEG dyploid FALSE
## 24017 FALSE t(9;22)+other BCR/ABL p190 NEG hyperd. FALSE
## 26003 FALSE del(p15/p16) BCR/ABL p210 NEG dyploid FALSE
## 28028 FALSE t(4;11) ALL1/AF4 <NA> NEG dyploid FALSE
## 28036 FALSE t(9;22) BCR/ABL p190 NEG dyploid FALSE
## 43001 FALSE t(9;22) BCR/ABL p190/p210 POS dyploid FALSE
## 49006 NA <NA> BCR/ABL p210 NEG dyploid FALSE
## 62003 FALSE t(9;22)+other BCR/ABL p210 NEG hyperd. FALSE
## 63001 NA <NA> ALL1/AF4 <NA> NEG dyploid FALSE
## 84004 NA <NA> BCR/ABL p190 NEG dyploid FALSE
## 16002 NA <NA> NEG <NA> NEG hyperd. FALSE
## 43015 TRUE normal NEG <NA> NEG dyploid FALSE
## relapse transplant f.u date last seen
## 03002 TRUE FALSE REL 10/15/1999
## 04007 TRUE FALSE REL 11/4/1997
## 08012 TRUE FALSE REL 4/9/1999
## 15004 TRUE FALSE REL 12/19/2000
## 16004 TRUE FALSE REL 12/9/1997
## 19005 TRUE FALSE REL 2/4/1998
## 20002 TRUE FALSE REL 12/15/1997
## 24005 TRUE FALSE REL 8/28/1997
## 24017 TRUE FALSE REL 2/22/2000
## 26003 TRUE FALSE REL 7/1/1998
## 28028 TRUE FALSE REL 10/20/1999
## 28036 TRUE FALSE REL 3/15/1999
## 43001 TRUE FALSE REL 6/28/1998
## 49006 TRUE FALSE REL 4/26/1999
## 62003 TRUE FALSE REL 8/8/2000
## 63001 TRUE FALSE REL 6/10/1998
## 84004 TRUE FALSE REL 1/25/1999
## 16002 TRUE FALSE REL 12/7/1999
## 43015 TRUE FALSE REL 3/15/20023.3.13 Indexing with
df2[df2$age > 40, ] # filter rows## cod diagnosis sex age BT remission CR date.cr
## 01005 1005 5/21/1997 M 53 B2 CR CR 8/6/1997
## 03002 3002 6/24/1998 F 52 B4 CR CR 8/17/1998
## 04007 4007 7/22/1997 M 57 B2 CR CR 9/17/1997
## 08012 8012 10/22/1998 M 55 B3 CR CR 1/9/1999
## 09008 9008 12/17/1999 M 41 B3 CR CR 2/15/2000
## 12006 12006 2/20/1997 M 46 B3 REF REF <NA>
## 12019 12019 9/4/1997 M 53 B2 CR CR 11/11/1997
## 14016 14016 5/27/1999 M 53 B2 <NA> <NA> <NA>
## 15004 15004 2/10/2000 M 44 B1 CR CR 4/3/2000
## 16004 16004 4/19/1997 F 58 B1 CR CR 7/15/1997
## 16009 16009 7/11/2000 F 43 B2 <NA> <NA> <NA>
## 19005 19005 11/15/1997 F 48 B1 CR CR 2/3/1998
## 20002 20002 5/9/1997 F 58 B2 CR CR 8/19/1997
## 24005 24005 1/3/1997 F 45 B1 CR CR 4/8/1997
## 24011 24011 8/5/1997 F 51 B2 <NA> DEATH IN INDUCTION <NA>
## 24017 24017 9/15/1998 M 57 B2 CR CR 12/7/1998
## NA <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## 26003 26003 2/18/1998 F 49 B4 CR CR 4/21/1998
## 27004 27004 10/20/1998 F 48 B2 REF REF <NA>
## 28007 28007 2/21/1997 F 47 B3 CR CR 4/7/1997
## 28021 28021 3/18/1998 F 54 B3 CR DEATH IN CR 5/22/1998
## 28028 28028 7/8/1998 M 47 B1 CR CR 9/3/1998
## 28032 28032 9/26/1998 F 52 B1 CR CR 10/30/1998
## 28036 28036 12/23/1998 M 52 B3 CR CR 3/8/1999
## NA.1 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## 30001 30001 1/16/1997 F 54 B3 <NA> DEATH IN INDUCTION <NA>
## NA.2 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## 43001 43001 11/14/1996 M 41 B1 CR CR 1/30/1997
## 43007 43007 10/14/1997 M 54 B4 CR CR 12/30/1997
## 49006 49006 8/12/1998 F 43 B2 CR CR 11/19/1998
## 57001 57001 1/29/1997 F 53 B3 <NA> DEATH IN INDUCTION <NA>
## 62001 62001 11/11/1997 F 50 B4 REF REF <NA>
## 62002 62002 1/15/1998 M 54 B4 <NA> DEATH IN INDUCTION <NA>
## 62003 62003 12/4/1998 M 53 B4 CR CR 1/28/1999
## 63001 63001 7/8/1997 M 49 B1 CR CR 9/2/1997
## 84004 84004 9/25/1998 M 50 B CR CR 12/1/1998
## NA.3 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## 02020 2020 3/23/2000 F 48 T2 <NA> DEATH IN INDUCTION <NA>
## 16002 16002 4/10/1997 M 50 T3 CR CR 6/10/1997
## 16007 16007 11/1/1998 M 41 T3 CR CR 11/5/1998
## 31015 31015 12/3/1998 M 48 T2 <NA> DEATH IN INDUCTION <NA>
## 43006 43006 6/17/1997 M 41 T2 REF REF <NA>
## 43015 43015 2/29/2000 M 52 T2 CR CR 6/8/2000
## NA.4 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## t(4;11) t(9;22) cyto.normal citog mol.biol fusion protein mdr
## 01005 FALSE TRUE FALSE t(9;22) BCR/ABL p210 NEG
## 03002 NA NA NA <NA> BCR/ABL p190 NEG
## 04007 FALSE FALSE FALSE del(6q) NEG <NA> NEG
## 08012 FALSE FALSE FALSE simple alt. NEG <NA> NEG
## 09008 FALSE TRUE FALSE t(9;22)+other BCR/ABL p190 NEG
## 12006 FALSE TRUE FALSE t(9;22) BCR/ABL p210 NEG
## 12019 FALSE FALSE TRUE normal NEG <NA> POS
## 14016 FALSE TRUE FALSE t(9;22) BCR/ABL p210 NEG
## 15004 TRUE FALSE FALSE t(4;11) ALL1/AF4 <NA> NEG
## 16004 TRUE FALSE FALSE t(4;11) ALL1/AF4 <NA> NEG
## 16009 NA NA NA <NA> NEG <NA> POS
## 19005 FALSE FALSE TRUE normal ALL1/AF4 <NA> NEG
## 20002 FALSE TRUE FALSE t(9;22)+other BCR/ABL p190 NEG
## 24005 TRUE FALSE FALSE t(4;11) ALL1/AF4 <NA> NEG
## 24011 FALSE TRUE FALSE t(9;22) BCR/ABL p210 POS
## 24017 FALSE TRUE FALSE t(9;22)+other BCR/ABL p190 NEG
## NA NA NA NA <NA> <NA> <NA> <NA>
## 26003 FALSE FALSE FALSE del(p15/p16) BCR/ABL p210 NEG
## 27004 FALSE TRUE FALSE t(9;22)+del(p15) BCR/ABL p190 NEG
## 28007 FALSE FALSE TRUE normal NEG <NA> NEG
## 28021 FALSE TRUE FALSE t(9;22)+other BCR/ABL p190/p210 NEG
## 28028 TRUE FALSE FALSE t(4;11) ALL1/AF4 <NA> NEG
## 28032 TRUE FALSE FALSE t(4;11) ALL1/AF4 <NA> NEG
## 28036 FALSE TRUE FALSE t(9;22) BCR/ABL p190 NEG
## NA.1 NA NA NA <NA> <NA> <NA> <NA>
## 30001 FALSE TRUE FALSE t(9;22)+other BCR/ABL p190 NEG
## NA.2 NA NA NA <NA> <NA> <NA> <NA>
## 43001 FALSE TRUE FALSE t(9;22) BCR/ABL p190/p210 POS
## 43007 FALSE FALSE TRUE normal NEG <NA> NEG
## 49006 NA NA NA <NA> BCR/ABL p210 NEG
## 57001 FALSE FALSE TRUE normal NEG <NA> NEG
## 62001 FALSE TRUE FALSE t(9;22)+other BCR/ABL <NA> NEG
## 62002 FALSE TRUE FALSE t(9;22)+other BCR/ABL <NA> NEG
## 62003 FALSE TRUE FALSE t(9;22)+other BCR/ABL p210 NEG
## 63001 NA NA NA <NA> ALL1/AF4 <NA> NEG
## 84004 NA NA NA <NA> BCR/ABL p190 NEG
## NA.3 NA NA NA <NA> <NA> <NA> <NA>
## 02020 FALSE FALSE FALSE complex alt. NEG <NA> NEG
## 16002 NA NA NA <NA> NEG <NA> NEG
## 16007 NA NA NA <NA> NEG <NA> NEG
## 31015 NA NA NA <NA> NEG <NA> POS
## 43006 FALSE FALSE FALSE simple alt. NEG <NA> POS
## 43015 FALSE FALSE TRUE normal NEG <NA> NEG
## NA.4 NA NA NA <NA> <NA> <NA> <NA>
## kinet ccr relapse transplant f.u date last seen
## 01005 dyploid FALSE FALSE TRUE BMT / DEATH IN CR <NA>
## 03002 dyploid FALSE TRUE FALSE REL 10/15/1999
## 04007 dyploid FALSE TRUE FALSE REL 11/4/1997
## 08012 dyploid FALSE TRUE FALSE REL 4/9/1999
## 09008 hyperd. TRUE FALSE TRUE BMT / CCR 00/09/01
## 12006 dyploid NA NA NA <NA> <NA>
## 12019 dyploid TRUE FALSE FALSE CCR 6/6/2002
## 14016 <NA> NA NA NA <NA> <NA>
## 15004 dyploid FALSE TRUE FALSE REL 12/19/2000
## 16004 dyploid FALSE TRUE FALSE REL 12/9/1997
## 16009 dyploid TRUE FALSE FALSE CCR / OFF 5/23/2002
## 19005 dyploid FALSE TRUE FALSE REL 2/4/1998
## 20002 dyploid FALSE TRUE FALSE REL 12/15/1997
## 24005 dyploid FALSE TRUE FALSE REL 8/28/1997
## 24011 dyploid NA NA NA <NA> <NA>
## 24017 hyperd. FALSE TRUE FALSE REL 2/22/2000
## NA <NA> NA NA NA <NA> <NA>
## 26003 dyploid FALSE TRUE FALSE REL 7/1/1998
## 27004 dyploid NA NA NA <NA> <NA>
## 28007 dyploid TRUE FALSE FALSE CCR 3/22/2002
## 28021 hyperd. FALSE FALSE FALSE DEATH IN CR (ICR) <NA>
## 28028 dyploid FALSE TRUE FALSE REL 10/20/1999
## 28032 dyploid TRUE FALSE FALSE CCR 5/16/2002
## 28036 dyploid FALSE TRUE FALSE REL 3/15/1999
## NA.1 <NA> NA NA NA <NA> <NA>
## 30001 hyperd. NA NA NA <NA> <NA>
## NA.2 <NA> NA NA NA <NA> <NA>
## 43001 dyploid FALSE TRUE FALSE REL 6/28/1998
## 43007 hyperd. TRUE FALSE FALSE CCR 5/29/2002
## 49006 dyploid FALSE TRUE FALSE REL 4/26/1999
## 57001 hyperd. NA NA NA <NA> <NA>
## 62001 hyperd. NA NA NA <NA> <NA>
## 62002 hyperd. NA NA NA <NA> <NA>
## 62003 hyperd. FALSE TRUE FALSE REL 8/8/2000
## 63001 dyploid FALSE TRUE FALSE REL 6/10/1998
## 84004 dyploid FALSE TRUE FALSE REL 1/25/1999
## NA.3 <NA> NA NA NA <NA> <NA>
## 02020 dyploid NA NA NA <NA> <NA>
## 16002 hyperd. FALSE TRUE FALSE REL 12/7/1999
## 16007 dyploid TRUE FALSE FALSE CCR 1/8/2002
## 31015 dyploid NA NA NA <NA> <NA>
## 43006 dyploid NA NA NA <NA> <NA>
## 43015 dyploid FALSE TRUE FALSE REL 3/15/2002
## NA.4 <NA> NA NA NA <NA> <NA>df2[df2$age > 40 & df2$relapse, ] # multiple conditions (same as df$Relapse == T)## cod diagnosis sex age BT remission CR date.cr t(4;11) t(9;22)
## 03002 3002 6/24/1998 F 52 B4 CR CR 8/17/1998 NA NA
## 04007 4007 7/22/1997 M 57 B2 CR CR 9/17/1997 FALSE FALSE
## 08012 8012 10/22/1998 M 55 B3 CR CR 1/9/1999 FALSE FALSE
## NA <NA> <NA> <NA> NA <NA> <NA> <NA> <NA> NA NA
## NA.1 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA> NA NA
## 15004 15004 2/10/2000 M 44 B1 CR CR 4/3/2000 TRUE FALSE
## 16004 16004 4/19/1997 F 58 B1 CR CR 7/15/1997 TRUE FALSE
## 19005 19005 11/15/1997 F 48 B1 CR CR 2/3/1998 FALSE FALSE
## 20002 20002 5/9/1997 F 58 B2 CR CR 8/19/1997 FALSE TRUE
## 24005 24005 1/3/1997 F 45 B1 CR CR 4/8/1997 TRUE FALSE
## NA.2 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA> NA NA
## 24017 24017 9/15/1998 M 57 B2 CR CR 12/7/1998 FALSE TRUE
## 26003 26003 2/18/1998 F 49 B4 CR CR 4/21/1998 FALSE FALSE
## NA.3 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA> NA NA
## 28028 28028 7/8/1998 M 47 B1 CR CR 9/3/1998 TRUE FALSE
## 28036 28036 12/23/1998 M 52 B3 CR CR 3/8/1999 FALSE TRUE
## NA.4 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA> NA NA
## NA.5 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA> NA NA
## NA.6 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA> NA NA
## 43001 43001 11/14/1996 M 41 B1 CR CR 1/30/1997 FALSE TRUE
## 49006 49006 8/12/1998 F 43 B2 CR CR 11/19/1998 NA NA
## NA.7 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA> NA NA
## NA.8 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA> NA NA
## NA.9 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA> NA NA
## 62003 62003 12/4/1998 M 53 B4 CR CR 1/28/1999 FALSE TRUE
## 63001 63001 7/8/1997 M 49 B1 CR CR 9/2/1997 NA NA
## 84004 84004 9/25/1998 M 50 B CR CR 12/1/1998 NA NA
## NA.10 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA> NA NA
## NA.11 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA> NA NA
## 16002 16002 4/10/1997 M 50 T3 CR CR 6/10/1997 NA NA
## NA.12 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA> NA NA
## NA.13 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA> NA NA
## 43015 43015 2/29/2000 M 52 T2 CR CR 6/8/2000 FALSE FALSE
## NA.14 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA> NA NA
## cyto.normal citog mol.biol fusion protein mdr kinet ccr
## 03002 NA <NA> BCR/ABL p190 NEG dyploid FALSE
## 04007 FALSE del(6q) NEG <NA> NEG dyploid FALSE
## 08012 FALSE simple alt. NEG <NA> NEG dyploid FALSE
## NA NA <NA> <NA> <NA> <NA> <NA> NA
## NA.1 NA <NA> <NA> <NA> <NA> <NA> NA
## 15004 FALSE t(4;11) ALL1/AF4 <NA> NEG dyploid FALSE
## 16004 FALSE t(4;11) ALL1/AF4 <NA> NEG dyploid FALSE
## 19005 TRUE normal ALL1/AF4 <NA> NEG dyploid FALSE
## 20002 FALSE t(9;22)+other BCR/ABL p190 NEG dyploid FALSE
## 24005 FALSE t(4;11) ALL1/AF4 <NA> NEG dyploid FALSE
## NA.2 NA <NA> <NA> <NA> <NA> <NA> NA
## 24017 FALSE t(9;22)+other BCR/ABL p190 NEG hyperd. FALSE
## 26003 FALSE del(p15/p16) BCR/ABL p210 NEG dyploid FALSE
## NA.3 NA <NA> <NA> <NA> <NA> <NA> NA
## 28028 FALSE t(4;11) ALL1/AF4 <NA> NEG dyploid FALSE
## 28036 FALSE t(9;22) BCR/ABL p190 NEG dyploid FALSE
## NA.4 NA <NA> <NA> <NA> <NA> <NA> NA
## NA.5 NA <NA> <NA> <NA> <NA> <NA> NA
## NA.6 NA <NA> <NA> <NA> <NA> <NA> NA
## 43001 FALSE t(9;22) BCR/ABL p190/p210 POS dyploid FALSE
## 49006 NA <NA> BCR/ABL p210 NEG dyploid FALSE
## NA.7 NA <NA> <NA> <NA> <NA> <NA> NA
## NA.8 NA <NA> <NA> <NA> <NA> <NA> NA
## NA.9 NA <NA> <NA> <NA> <NA> <NA> NA
## 62003 FALSE t(9;22)+other BCR/ABL p210 NEG hyperd. FALSE
## 63001 NA <NA> ALL1/AF4 <NA> NEG dyploid FALSE
## 84004 NA <NA> BCR/ABL p190 NEG dyploid FALSE
## NA.10 NA <NA> <NA> <NA> <NA> <NA> NA
## NA.11 NA <NA> <NA> <NA> <NA> <NA> NA
## 16002 NA <NA> NEG <NA> NEG hyperd. FALSE
## NA.12 NA <NA> <NA> <NA> <NA> <NA> NA
## NA.13 NA <NA> <NA> <NA> <NA> <NA> NA
## 43015 TRUE normal NEG <NA> NEG dyploid FALSE
## NA.14 NA <NA> <NA> <NA> <NA> <NA> NA
## relapse transplant f.u date last seen
## 03002 TRUE FALSE REL 10/15/1999
## 04007 TRUE FALSE REL 11/4/1997
## 08012 TRUE FALSE REL 4/9/1999
## NA NA NA <NA> <NA>
## NA.1 NA NA <NA> <NA>
## 15004 TRUE FALSE REL 12/19/2000
## 16004 TRUE FALSE REL 12/9/1997
## 19005 TRUE FALSE REL 2/4/1998
## 20002 TRUE FALSE REL 12/15/1997
## 24005 TRUE FALSE REL 8/28/1997
## NA.2 NA NA <NA> <NA>
## 24017 TRUE FALSE REL 2/22/2000
## 26003 TRUE FALSE REL 7/1/1998
## NA.3 NA NA <NA> <NA>
## 28028 TRUE FALSE REL 10/20/1999
## 28036 TRUE FALSE REL 3/15/1999
## NA.4 NA NA <NA> <NA>
## NA.5 NA NA <NA> <NA>
## NA.6 NA NA <NA> <NA>
## 43001 TRUE FALSE REL 6/28/1998
## 49006 TRUE FALSE REL 4/26/1999
## NA.7 NA NA <NA> <NA>
## NA.8 NA NA <NA> <NA>
## NA.9 NA NA <NA> <NA>
## 62003 TRUE FALSE REL 8/8/2000
## 63001 TRUE FALSE REL 6/10/1998
## 84004 TRUE FALSE REL 1/25/1999
## NA.10 NA NA <NA> <NA>
## NA.11 NA NA <NA> <NA>
## 16002 TRUE FALSE REL 12/7/1999
## NA.12 NA NA <NA> <NA>
## NA.13 NA NA <NA> <NA>
## 43015 TRUE FALSE REL 3/15/2002
## NA.14 NA NA <NA> <NA>df2[, c("age", "BT")] # select columns## age BT
## 01005 53 B2
## 01010 19 B2
## 03002 52 B4
## 04006 38 B1
## 04007 57 B2
## 04008 17 B1
## 04010 18 B1
## 04016 16 B1
## 06002 15 B2
## 08001 40 B2
## 08011 33 B3
## 08012 55 B3
## 08018 5 B3
## 08024 18 B2
## 09008 41 B3
## 09017 27 B
## 11005 27 B2
## 12006 46 B3
## 12007 37 B2
## 12012 36 B3
## 12019 53 B2
## 12026 39 B2
## 14016 53 B2
## 15001 20 B1
## 15004 44 B1
## 15005 28 B2
## 16004 58 B1
## 16009 43 B2
## 19005 48 B1
## 20002 58 B2
## 22009 19 B
## 22010 26 B
## 22011 19 B2
## 22013 32 B2
## 24001 17 B2
## 24005 45 B1
## 24008 20 B2
## 24010 16 B2
## 24011 51 B2
## 24017 57 B2
## 24018 29 B2
## 24019 16 B4
## 24022 32 B4
## 25003 15 B2
## 25006 NA B2
## 26001 21 B2
## 26003 49 B4
## 26005 38 B2
## 26008 17 B1
## 27003 26 B2
## 27004 48 B2
## 28001 16 B3
## 28003 18 B4
## 28005 17 B3
## 28006 22 B3
## 28007 47 B3
## 28019 21 B4
## 28021 54 B3
## 28023 26 B3
## 28024 19 B1
## 28028 47 B1
## 28031 18 B1
## 28032 52 B1
## 28035 27 B3
## 28036 52 B3
## 28037 18 B3
## 28042 18 B3
## 28043 23 B3
## 28044 16 B3
## 28047 NA B3
## 30001 54 B3
## 31007 25 B1
## 31011 31 B3
## 33005 19 B1
## 36001 24 B4
## 36002 23 B2
## 37013 NA B2
## 43001 41 B1
## 43004 37 B3
## 43007 54 B4
## 43012 18 B4
## 48001 19 B2
## 49006 43 B2
## 57001 53 B3
## 62001 50 B4
## 62002 54 B4
## 62003 53 B4
## 63001 49 B1
## 64001 20 B2
## 64002 26 B2
## 65005 22 B2
## 68001 36 B1
## 68003 27 B2
## 84004 50 B
## LAL5 NA B
## 01003 31 T
## 01007 16 T3
## 02020 48 T2
## 04018 17 T2
## 09002 40 T3
## 10005 22 T2
## 11002 30 T
## 12008 18 T4
## 15006 22 T2
## 16002 50 T3
## 16007 41 T3
## 17003 40 T
## 18001 28 T2
## 19002 25 T3
## 19008 16 T2
## 19014 31 T2
## 19017 14 T2
## 20005 24 T1
## 24006 19 T4
## 26009 37 T
## 28008 23 T2
## 28009 30 T3
## 31015 48 T2
## 37001 22 T2
## 43006 41 T2
## 43015 52 T2
## 44001 32 T3
## 49004 24 T3
## 56007 37 T3
## 64005 19 T2
## 65003 30 T3
## 83001 29 T2
## LAL4 NA Tdf <- df2[df2$sex == "F", ] # female patients only (#Assignment with condition)3.3.14 with()
dfrt2 <- with(df2, df2[age > 40 & relapse == TRUE, ]) #for cleaner syntax
df2[which(df2$age > 40 & df2$relapse == TRUE), ] # more cleanr syntax## cod diagnosis sex age BT remission CR date.cr t(4;11) t(9;22)
## 03002 3002 6/24/1998 F 52 B4 CR CR 8/17/1998 NA NA
## 04007 4007 7/22/1997 M 57 B2 CR CR 9/17/1997 FALSE FALSE
## 08012 8012 10/22/1998 M 55 B3 CR CR 1/9/1999 FALSE FALSE
## 15004 15004 2/10/2000 M 44 B1 CR CR 4/3/2000 TRUE FALSE
## 16004 16004 4/19/1997 F 58 B1 CR CR 7/15/1997 TRUE FALSE
## 19005 19005 11/15/1997 F 48 B1 CR CR 2/3/1998 FALSE FALSE
## 20002 20002 5/9/1997 F 58 B2 CR CR 8/19/1997 FALSE TRUE
## 24005 24005 1/3/1997 F 45 B1 CR CR 4/8/1997 TRUE FALSE
## 24017 24017 9/15/1998 M 57 B2 CR CR 12/7/1998 FALSE TRUE
## 26003 26003 2/18/1998 F 49 B4 CR CR 4/21/1998 FALSE FALSE
## 28028 28028 7/8/1998 M 47 B1 CR CR 9/3/1998 TRUE FALSE
## 28036 28036 12/23/1998 M 52 B3 CR CR 3/8/1999 FALSE TRUE
## 43001 43001 11/14/1996 M 41 B1 CR CR 1/30/1997 FALSE TRUE
## 49006 49006 8/12/1998 F 43 B2 CR CR 11/19/1998 NA NA
## 62003 62003 12/4/1998 M 53 B4 CR CR 1/28/1999 FALSE TRUE
## 63001 63001 7/8/1997 M 49 B1 CR CR 9/2/1997 NA NA
## 84004 84004 9/25/1998 M 50 B CR CR 12/1/1998 NA NA
## 16002 16002 4/10/1997 M 50 T3 CR CR 6/10/1997 NA NA
## 43015 43015 2/29/2000 M 52 T2 CR CR 6/8/2000 FALSE FALSE
## cyto.normal citog mol.biol fusion protein mdr kinet ccr
## 03002 NA <NA> BCR/ABL p190 NEG dyploid FALSE
## 04007 FALSE del(6q) NEG <NA> NEG dyploid FALSE
## 08012 FALSE simple alt. NEG <NA> NEG dyploid FALSE
## 15004 FALSE t(4;11) ALL1/AF4 <NA> NEG dyploid FALSE
## 16004 FALSE t(4;11) ALL1/AF4 <NA> NEG dyploid FALSE
## 19005 TRUE normal ALL1/AF4 <NA> NEG dyploid FALSE
## 20002 FALSE t(9;22)+other BCR/ABL p190 NEG dyploid FALSE
## 24005 FALSE t(4;11) ALL1/AF4 <NA> NEG dyploid FALSE
## 24017 FALSE t(9;22)+other BCR/ABL p190 NEG hyperd. FALSE
## 26003 FALSE del(p15/p16) BCR/ABL p210 NEG dyploid FALSE
## 28028 FALSE t(4;11) ALL1/AF4 <NA> NEG dyploid FALSE
## 28036 FALSE t(9;22) BCR/ABL p190 NEG dyploid FALSE
## 43001 FALSE t(9;22) BCR/ABL p190/p210 POS dyploid FALSE
## 49006 NA <NA> BCR/ABL p210 NEG dyploid FALSE
## 62003 FALSE t(9;22)+other BCR/ABL p210 NEG hyperd. FALSE
## 63001 NA <NA> ALL1/AF4 <NA> NEG dyploid FALSE
## 84004 NA <NA> BCR/ABL p190 NEG dyploid FALSE
## 16002 NA <NA> NEG <NA> NEG hyperd. FALSE
## 43015 TRUE normal NEG <NA> NEG dyploid FALSE
## relapse transplant f.u date last seen
## 03002 TRUE FALSE REL 10/15/1999
## 04007 TRUE FALSE REL 11/4/1997
## 08012 TRUE FALSE REL 4/9/1999
## 15004 TRUE FALSE REL 12/19/2000
## 16004 TRUE FALSE REL 12/9/1997
## 19005 TRUE FALSE REL 2/4/1998
## 20002 TRUE FALSE REL 12/15/1997
## 24005 TRUE FALSE REL 8/28/1997
## 24017 TRUE FALSE REL 2/22/2000
## 26003 TRUE FALSE REL 7/1/1998
## 28028 TRUE FALSE REL 10/20/1999
## 28036 TRUE FALSE REL 3/15/1999
## 43001 TRUE FALSE REL 6/28/1998
## 49006 TRUE FALSE REL 4/26/1999
## 62003 TRUE FALSE REL 8/8/2000
## 63001 TRUE FALSE REL 6/10/1998
## 84004 TRUE FALSE REL 1/25/1999
## 16002 TRUE FALSE REL 12/7/1999
## 43015 TRUE FALSE REL 3/15/20023.3.15 match() / %in% (matching values)
dfrt <- df2[df2$BT %in% c("B2", "B3"), ]3.3.16 Logical indexing directly
df2[df2$relapse == F | df2$sex == "F", ]## cod diagnosis sex age BT remission CR date.cr
## 01005 1005 5/21/1997 M 53 B2 CR CR 8/6/1997
## 03002 3002 6/24/1998 F 52 B4 CR CR 8/17/1998
## 04010 4010 10/30/1997 F 18 B1 CR CR 1/7/1998
## 08011 8011 8/21/1998 M 33 B3 CR CR 10/8/1998
## NA <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## 09008 9008 12/17/1999 M 41 B3 CR CR 2/15/2000
## 09017 9017 2/3/2000 F 27 B CR CR 3/23/2000
## 11005 11005 6/1/1998 M 27 B2 CR DEATH IN CR 8/3/1998
## NA.1 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## 12012 12012 5/21/1997 F 36 B3 REF REF <NA>
## 12019 12019 9/4/1997 M 53 B2 CR CR 11/11/1997
## 12026 12026 5/29/1998 M 39 B2 REF REF <NA>
## NA.2 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## 15001 15001 9/3/1997 M 20 B1 CR CR 11/11/1997
## 16004 16004 4/19/1997 F 58 B1 CR CR 7/15/1997
## 16009 16009 7/11/2000 F 43 B2 <NA> <NA> <NA>
## 19005 19005 11/15/1997 F 48 B1 CR CR 2/3/1998
## 20002 20002 5/9/1997 F 58 B2 CR CR 8/19/1997
## 22009 22009 8/10/1999 F 19 B <NA> <NA> <NA>
## 22010 22010 12/31/1999 F 26 B <NA> <NA> <NA>
## 22011 22011 4/7/2000 M 19 B2 CR CR 5/19/2000
## NA.3 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## 24001 24001 10/4/1996 F 17 B2 CR CR 12/20/1996
## 24005 24005 1/3/1997 F 45 B1 CR CR 4/8/1997
## 24008 24008 5/14/1997 F 20 B2 CR CR 7/31/1997
## 24010 24010 6/3/1997 F 16 B2 CR CR 8/11/1997
## 24011 24011 8/5/1997 F 51 B2 <NA> DEATH IN INDUCTION <NA>
## 24018 24018 2/18/1999 F 29 B2 CR CR 5/4/1999
## 24022 24022 12/21/1999 F 32 B4 REF REF <NA>
## 25003 25003 5/22/1998 M 15 B2 CR CR 8/4/1998
## 25006 25006 3/18/2000 <NA> NA B2 CR CR 5/8/2000
## 26001 26001 9/27/1997 M 21 B2 CR CR 12/11/1997
## 26003 26003 2/18/1998 F 49 B4 CR CR 4/21/1998
## 26008 26008 8/25/1999 F 17 B1 CR CR 10/14/1999
## 27003 27003 1/17/1998 F 26 B2 CR CR 3/16/1998
## 27004 27004 10/20/1998 F 48 B2 REF REF <NA>
## NA.4 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## 28003 28003 11/28/1996 M 18 B4 CR CR 1/17/1997
## 28007 28007 2/21/1997 F 47 B3 CR CR 4/7/1997
## 28019 28019 2/10/1998 M 21 B4 CR CR 4/2/1998
## 28021 28021 3/18/1998 F 54 B3 CR DEATH IN CR 5/22/1998
## 28024 28024 4/19/1998 F 19 B1 CR CR 6/17/1998
## 28032 28032 9/26/1998 F 52 B1 CR CR 10/30/1998
## 28035 28035 12/21/1998 M 27 B3 CR CR 2/12/1999
## 30001 30001 1/16/1997 F 54 B3 <NA> DEATH IN INDUCTION <NA>
## 33005 33005 2/10/1998 F 19 B1 CR CR 4/29/1998
## 36001 36001 9/29/1997 F 24 B4 CR CR 12/5/1997
## NA.5 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## 43004 43004 2/4/1997 F 37 B3 CR CR 4/1/1997
## 43007 43007 10/14/1997 M 54 B4 CR CR 12/30/1997
## 48001 48001 3/22/1997 M 19 B2 CR CR 5/20/1997
## 49006 49006 8/12/1998 F 43 B2 CR CR 11/19/1998
## 57001 57001 1/29/1997 F 53 B3 <NA> DEATH IN INDUCTION <NA>
## 62001 62001 11/11/1997 F 50 B4 REF REF <NA>
## NA.6 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## 64002 64002 10/21/1997 F 26 B2 CR CR 1/21/1998
## NA.7 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## 68001 68001 5/15/1997 M 36 B1 CR CR 7/22/1997
## 68003 68003 4/11/2000 F 27 B2 <NA> DEATH IN INDUCTION <NA>
## NA.8 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## 01007 1007 9/30/1998 F 16 T3 CR CR 11/30/1998
## 02020 2020 3/23/2000 F 48 T2 <NA> DEATH IN INDUCTION <NA>
## 04018 4018 3/24/2000 M 17 T2 CR CR 5/23/2000
## 09002 9002 5/14/1998 F 40 T3 CR CR 7/21/1998
## NA.9 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## 16007 16007 11/1/1998 M 41 T3 CR CR 11/5/1998
## 17003 17003 4/8/1997 F 40 T REF REF <NA>
## 18001 18001 4/23/1997 F 28 T2 REF REF <NA>
## 19008 19008 4/29/1998 F 16 T2 REF REF <NA>
## 20005 20005 3/15/2000 M 24 T1 CR CR 5/5/2000
## 24006 24006 1/14/1997 F 19 T4 CR CR not known
## 28008 28008 3/27/1997 M 23 T2 CR CR 5/27/1997
## 28009 28009 4/19/1997 F 30 T3 CR CR 6/13/1997
## NA.10 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## NA.11 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## 49004 49004 9/18/1997 M 24 T3 CR CR 11/11/1997
## 56007 56007 8/6/1999 M 37 T3 CR CR 9/24/1999
## NA.12 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## 83001 83001 10/23/1998 M 29 T2 CR CR 12/21/1998
## NA.13 <NA> <NA> <NA> NA <NA> <NA> <NA> <NA>
## t(4;11) t(9;22) cyto.normal citog mol.biol fusion protein mdr
## 01005 FALSE TRUE FALSE t(9;22) BCR/ABL p210 NEG
## 03002 NA NA NA <NA> BCR/ABL p190 NEG
## 04010 FALSE FALSE FALSE complex alt. NEG <NA> POS
## 08011 FALSE FALSE FALSE del(p15/p16) BCR/ABL p190/p210 NEG
## NA NA NA NA <NA> <NA> <NA> <NA>
## 09008 FALSE TRUE FALSE t(9;22)+other BCR/ABL p190 NEG
## 09017 FALSE FALSE TRUE normal NEG <NA> NEG
## 11005 FALSE FALSE FALSE del(7q) + altro BCR/ABL p190 NEG
## NA.1 NA NA NA <NA> <NA> <NA> <NA>
## 12012 FALSE TRUE FALSE t(9;22) BCR/ABL p190 NEG
## 12019 FALSE FALSE TRUE normal NEG <NA> POS
## 12026 FALSE TRUE FALSE t(9;22) BCR/ABL p190/p210 <NA>
## NA.2 NA NA NA <NA> <NA> <NA> <NA>
## 15001 FALSE FALSE TRUE normal NEG <NA> NEG
## 16004 TRUE FALSE FALSE t(4;11) ALL1/AF4 <NA> NEG
## 16009 NA NA NA <NA> NEG <NA> POS
## 19005 FALSE FALSE TRUE normal ALL1/AF4 <NA> NEG
## 20002 FALSE TRUE FALSE t(9;22)+other BCR/ABL p190 NEG
## 22009 FALSE FALSE FALSE simple alt. NEG <NA> NEG
## 22010 FALSE TRUE FALSE t(9;22) BCR/ABL p190/p210 NEG
## 22011 FALSE FALSE TRUE normal NEG <NA> NEG
## NA.3 NA NA NA <NA> <NA> <NA> <NA>
## 24001 NA NA NA <NA> BCR/ABL p190 NEG
## 24005 TRUE FALSE FALSE t(4;11) ALL1/AF4 <NA> NEG
## 24008 NA NA NA <NA> NEG <NA> NEG
## 24010 FALSE TRUE FALSE t(9;22) BCR/ABL p190/p210 NEG
## 24011 FALSE TRUE FALSE t(9;22) BCR/ABL p210 POS
## 24018 NA NA NA <NA> NEG <NA> POS
## 24022 FALSE TRUE FALSE t(9;22) BCR/ABL p190 POS
## 25003 FALSE FALSE FALSE simple alt. NEG <NA> POS
## 25006 NA NA NA <NA> NEG <NA> NEG
## 26001 NA NA NA <NA> NEG <NA> POS
## 26003 FALSE FALSE FALSE del(p15/p16) BCR/ABL p210 NEG
## 26008 FALSE FALSE TRUE normal ALL1/AF4 <NA> NEG
## 27003 NA NA NA <NA> BCR/ABL p190/p210 POS
## 27004 FALSE TRUE FALSE t(9;22)+del(p15) BCR/ABL p190 NEG
## NA.4 NA NA NA <NA> <NA> <NA> <NA>
## 28003 NA NA NA <NA> E2A/PBX1 <NA> NEG
## 28007 FALSE FALSE TRUE normal NEG <NA> NEG
## 28019 NA NA NA <NA> BCR/ABL p190 NEG
## 28021 FALSE TRUE FALSE t(9;22)+other BCR/ABL p190/p210 NEG
## 28024 FALSE FALSE FALSE complex alt. NEG <NA> NEG
## 28032 TRUE FALSE FALSE t(4;11) ALL1/AF4 <NA> NEG
## 28035 NA NA NA <NA> NEG <NA> POS
## 30001 FALSE TRUE FALSE t(9;22)+other BCR/ABL p190 NEG
## 33005 FALSE FALSE FALSE complex alt. NEG <NA> NEG
## 36001 FALSE FALSE TRUE normal E2A/PBX1 <NA> NEG
## NA.5 NA NA NA <NA> <NA> <NA> <NA>
## 43004 NA NA NA <NA> NEG <NA> NEG
## 43007 FALSE FALSE TRUE normal NEG <NA> NEG
## 48001 FALSE FALSE FALSE complex alt. NEG <NA> NEG
## 49006 NA NA NA <NA> BCR/ABL p210 NEG
## 57001 FALSE FALSE TRUE normal NEG <NA> NEG
## 62001 FALSE TRUE FALSE t(9;22)+other BCR/ABL <NA> NEG
## NA.6 NA NA NA <NA> <NA> <NA> <NA>
## 64002 NA NA NA <NA> NEG <NA> NEG
## NA.7 NA NA NA <NA> <NA> <NA> <NA>
## 68001 FALSE FALSE TRUE normal NEG <NA> NEG
## 68003 FALSE TRUE FALSE t(9;22)+other BCR/ABL p190 NEG
## NA.8 NA NA NA <NA> <NA> <NA> <NA>
## 01007 FALSE FALSE FALSE simple alt. NUP-98 <NA> NEG
## 02020 FALSE FALSE FALSE complex alt. NEG <NA> NEG
## 04018 FALSE FALSE FALSE simple alt. NEG <NA> NEG
## 09002 NA NA NA <NA> NEG <NA> NEG
## NA.9 NA NA NA <NA> <NA> <NA> <NA>
## 16007 NA NA NA <NA> NEG <NA> NEG
## 17003 NA NA NA <NA> NEG <NA> POS
## 18001 NA NA NA <NA> NEG <NA> NEG
## 19008 FALSE FALSE TRUE normal NEG <NA> POS
## 20005 NA NA NA <NA> NEG <NA> NEG
## 24006 FALSE FALSE FALSE simple alt. NEG <NA> NEG
## 28008 FALSE FALSE TRUE normal NEG <NA> NEG
## 28009 NA NA NA <NA> NEG <NA> NEG
## NA.10 NA NA NA <NA> <NA> <NA> <NA>
## NA.11 NA NA NA <NA> <NA> <NA> <NA>
## 49004 FALSE FALSE FALSE del(7q) NEG <NA> POS
## 56007 NA NA NA <NA> NEG <NA> NEG
## NA.12 NA NA NA <NA> <NA> <NA> <NA>
## 83001 FALSE FALSE FALSE complex alt. NEG <NA> NEG
## NA.13 NA NA NA <NA> <NA> <NA> <NA>
## kinet ccr relapse transplant f.u date last seen
## 01005 dyploid FALSE FALSE TRUE BMT / DEATH IN CR <NA>
## 03002 dyploid FALSE TRUE FALSE REL 10/15/1999
## 04010 hyperd. FALSE TRUE FALSE REL 3/5/1998
## 08011 dyploid FALSE FALSE TRUE BMT / DEATH IN CR <NA>
## NA <NA> NA NA NA <NA> <NA>
## 09008 hyperd. TRUE FALSE TRUE BMT / CCR 00/09/01
## 09017 dyploid FALSE TRUE FALSE REL 9/11/2001
## 11005 dyploid FALSE FALSE FALSE DEATH IN CR <NA>
## NA.1 <NA> NA NA NA <NA> <NA>
## 12012 dyploid NA NA NA <NA> <NA>
## 12019 dyploid TRUE FALSE FALSE CCR 6/6/2002
## 12026 dyploid FALSE FALSE FALSE DEATH IN CR <NA>
## NA.2 <NA> NA NA NA <NA> <NA>
## 15001 dyploid TRUE FALSE FALSE CCR 6/21/2002
## 16004 dyploid FALSE TRUE FALSE REL 12/9/1997
## 16009 dyploid TRUE FALSE FALSE CCR / OFF 5/23/2002
## 19005 dyploid FALSE TRUE FALSE REL 2/4/1998
## 20002 dyploid FALSE TRUE FALSE REL 12/15/1997
## 22009 dyploid NA NA NA <NA> <NA>
## 22010 dyploid NA NA NA <NA> <NA>
## 22011 dyploid TRUE FALSE FALSE CCR 7/31/2002
## NA.3 <NA> NA NA NA <NA> <NA>
## 24001 dyploid FALSE TRUE FALSE REL 2/10/1997
## 24005 dyploid FALSE TRUE FALSE REL 8/28/1997
## 24008 dyploid FALSE FALSE TRUE BMT / CCR 00/09/20+T12501
## 24010 dyploid FALSE TRUE TRUE BMT / REL 8/24/1998
## 24011 dyploid NA NA NA <NA> <NA>
## 24018 dyploid FALSE TRUE FALSE REL 7/22/2000
## 24022 dyploid NA NA NA <NA> <NA>
## 25003 dyploid TRUE FALSE FALSE CCR 6/10/2002
## 25006 <NA> TRUE FALSE FALSE CCR 3/3/2002
## 26001 dyploid TRUE FALSE FALSE CCR 7/31/2002
## 26003 dyploid FALSE TRUE FALSE REL 7/1/1998
## 26008 dyploid FALSE TRUE FALSE REL 6/26/2000
## 27003 dyploid FALSE TRUE FALSE REL 5/6/1998
## 27004 dyploid NA NA NA <NA> <NA>
## NA.4 <NA> NA NA NA <NA> <NA>
## 28003 hyperd. TRUE FALSE FALSE CCR 12/31/2002
## 28007 dyploid TRUE FALSE FALSE CCR 3/22/2002
## 28019 hyperd. TRUE FALSE TRUE BMT / CCR 3/21/2001
## 28021 hyperd. FALSE FALSE FALSE DEATH IN CR (ICR) <NA>
## 28024 hyperd. TRUE FALSE FALSE CCR 12/31/2002
## 28032 dyploid TRUE FALSE FALSE CCR 5/16/2002
## 28035 hyperd. TRUE FALSE FALSE CCR 5/20/2002
## 30001 hyperd. NA NA NA <NA> <NA>
## 33005 dyploid TRUE FALSE FALSE CCR 6/28/2002
## 36001 dyploid FALSE TRUE FALSE REL 1/7/1998
## NA.5 <NA> NA NA NA <NA> <NA>
## 43004 dyploid TRUE FALSE FALSE CCR 3/20/2001
## 43007 hyperd. TRUE FALSE FALSE CCR 5/29/2002
## 48001 hyperd. FALSE FALSE FALSE MUD / DEATH IN CR 12/18/1998
## 49006 dyploid FALSE TRUE FALSE REL 4/26/1999
## 57001 hyperd. NA NA NA <NA> <NA>
## 62001 hyperd. NA NA NA <NA> <NA>
## NA.6 <NA> NA NA NA <NA> <NA>
## 64002 hyperd. FALSE FALSE TRUE BMT / DEATH IN CR <NA>
## NA.7 <NA> NA NA NA <NA> <NA>
## 68001 dyploid TRUE FALSE FALSE CCR 5/10/2002
## 68003 <NA> NA NA NA <NA> <NA>
## NA.8 <NA> NA NA NA <NA> <NA>
## 01007 hyperd. FALSE FALSE TRUE BMT / DEATH IN CR <NA>
## 02020 dyploid NA NA NA <NA> <NA>
## 04018 dyploid TRUE FALSE FALSE CCR 5/14/2001
## 09002 dyploid FALSE TRUE FALSE REL / SNC 9/14/1999
## NA.9 <NA> NA NA NA <NA> <NA>
## 16007 dyploid TRUE FALSE FALSE CCR 1/8/2002
## 17003 dyploid NA NA NA <NA> <NA>
## 18001 hyperd. NA NA NA <NA> <NA>
## 19008 dyploid NA NA NA <NA> <NA>
## 20005 dyploid TRUE FALSE FALSE CCR 3/20/2002
## 24006 dyploid TRUE FALSE FALSE CCR 6/5/2002
## 28008 hyperd. TRUE FALSE FALSE CCR 4/9/2002
## 28009 dyploid FALSE TRUE FALSE REL 6/30/1998
## NA.10 <NA> NA NA NA <NA> <NA>
## NA.11 <NA> NA NA NA <NA> <NA>
## 49004 dyploid TRUE FALSE FALSE CCR 6/14/2001
## 56007 dyploid TRUE FALSE FALSE CCR 1/26/2001
## NA.12 <NA> NA NA NA <NA> <NA>
## 83001 hyperd. TRUE FALSE FALSE CCR 5/24/2002
## NA.13 <NA> NA NA NA <NA> <NA>3.4 Lab 1B Tasks
# Task 1
# Patients younger than 20
subset(ALL_df, age < 20)
# Task 2
# Age and Sex for patients with BT = "B2"
subset(ALL_df, BT == "B2", select = c(age, sex))
# Task 3
# Male patients older than 40
subset(ALL_df, sex == "M" & age > 40)
# Female OR Relapse = Yes
subset(ALL_df, sex == "F" | relapse == T)
# Mini-Challenge
# Male + Relapse + Age > 30
subset(ALL_df, sex == "M" & relapse == T & age > 30)
#OR
ALL_df[ALL_df$sex == "M" & ALL_df$relapse == T & ALL_df$age > 30, ]4 Module 2
4.1 Lecture
4.1.1 2A
4.1.2 2B
4.2 Lab 2A
4.2.1 Read data in to R
read CSV - base functions
bp <- read.csv2("Desktop/R/data/BloodPressure_Data.csv") # no sepqration
# take a quick look at the data
head(bp)bp <- read.csv2("Desktop/R/data/BloodPressure_Data.csv", sep = ",") # no sepqration
# take another look at the data
head(bp)
str(bp)readr functions
library(readr)Read the CSV file
bp_data <- read_csv("Desktop/R/data/BloodPressure_Data.csv")Take a quick look at the data
head(bp_data)
str(bp_data)Work with date
library(readr)
library("lubridate")read ALL data
bp <- read.csv2("Desktop/R/data/BloodPressure_wDates.csv", sep = ",")Convert date column and extract year
bp$Date <- ymd(bp$Date)
bp$Year <- year(bp$Date)Filtering blood pressure patients by year and gender
subset(bp, Year == 2003 & Gender == "f")4.2.2 Conditions and loops
If {} else {} statement
if (condition) {
# code if TRUE
} else {
# code if FALSE
}# If else example
age <- 55
if (age > 50) {
print("Older patient")
} else {
print("Younger patient")
}# If {} else if {} else statement
if (condition1) {
# code if condition1 is TRUE
} else if (condition2) {
# code if condition2 is TRUE
} else {
# code if none are TRUE
}# If else if example
age <- 35
if (age < 18) {
print("Child")
} else if (age >= 18 & age < 60) {
print("Adult")
} else {
print("Senior")
}# for loops
for (i in 1:5) {
print(i)
}# for loop example
patients <- c("P1", "P2", "P3")
for (p in patients) {
print(paste("Processing:", p))
}# the apply () family vs. loops
# Using a for loop
m <- matrix(1:9, nrow=3)
row_sums <- c()
for (i in 1:nrow(m)) {
row_sums[i] <- sum(m[i, ])
}# Using apply()
row_sums2 <- apply(m, 1, sum)# the apply() family
# apply()
apply(m, 1, sum) # row sums
apply(m, 2, mean) # column means# lapply()
lapply(list(1:3, 4:6), mean)# sapply()
sapply(list(1:3, 4:6), mean)# lapply()
lapply(list(1:3, 4:6), mean)# tapply()
ages <- c(21, 25, 30, 40, 35)
gender <- c("M", "M", "F", "F", "M")
tapply(ages, gender, mean) # mean age by gender# mapply()
nums1 <- 1:5
nums2 <- 6:10
mapply(sum, nums1, nums2) # adds 1+6, 2+7, … 5+104.3 Lab 2A Tasks
Task 1 – Basic Filtering
#Use a for loop with if/else conditions
Go through each row of the dataset and:
Print a message if the patient has High BP (> 140) # Tip: use the paste function,
Print a message if the patient has Low BP (< 90)
Otherwise, mark them as Normal
# read data
bp_data <- read.csv2("Desktop/R/data/BloodPressure_wDates.csv", sep = ",")
# Use for loop
for (i in 1:nrow(bp_data)) {
if (bp_data$BloodPressure[i] > 140) {
print(paste("Patient", bp_data$ID[i], "has HIGH blood pressure"))
} else if (bp_data$BloodPressure[i] < 90) {
print(paste("Patient", bp_data$ID[i], "has LOW blood pressure"))
} else {
print(paste("Patient", bp_data$ID[i], "is NORMAL"))
}
}
# Use apply() instead of loops
bp_data$BP_Status <- apply(bp_data, 1, function(row) {
if (as.numeric(row["BloodPressure"]) > 140) {
"HIGH"
} else if (as.numeric(row["BloodPressure"]) < 90) {
"LOW"
} else {
"NORMAL"
}
})4.4 Lab 2B
4.4.1 Basic plotting in R
Plot multiple panels in one plot
par(mfrow = c(3, 1))
layout(matrix(c(1, 1, 2, 3), nrow = 2, byrow = TRUE))Histogram of Blood Pressure
hist(bp_data$BloodPressure, main="Blood Pressure Distribution",
xlab="Blood Pressure", col="lightblue")Boxplot of BP by Gender
boxplot(BloodPressure ~ Gender, data=bp_data,
main="BP by Gender", xlab="Gender", ylab="Blood Pressure")Scatterplot Age vs BP
plot(bp_data$Age, bp_data$BloodPressure,
main="Age vs Blood Pressure", xlab="Age", ylab="BP")4.4.2 ggplot2
# example syntax
#ggplot(data, aes(x, y)) + geom_*()library(ggplot2)
# Scatterplot: Age vs Blood Pressure
ggplot(bp_data, aes(x=Age, y=BloodPressure)) +
geom_point()boxplot
ggplot(bp_data, aes(x=Group, y=BloodPressure)) +
geom_boxplot()Customizing ggplot2
ggplot(bp_data, aes(x = Age, y = BloodPressure)) +
geom_point(color = "blue") +
labs(
title = "Age vs Blood Pressure",
x = "Patient Age",
y = "BP (mmHg)"
) +
theme_minimal() # Save last plot as PNG
ggsave("Age_BP_Scatter.png", width=6, height=4)# Save specific plot object
p <- ggplot(bp_data, aes(x=Age, y=BloodPressure)) +
geom_point()
ggsave("data/scatter_plot.png", plot=p)4.5 Lab 2B Tasks
ggplot hands on tasks
library(lubridate)
library(ggplot2)
library(patchwork)Load data
bp_data <- read.csv2("data/BloodPressure_wDates.csv", sep = ",")Get the year in a new column
bp_data$Year <- year(bp_data$Date)- Bar plot: patient counts per group
# ggplot hands on tasks
ggplot(bp_data, aes(x=Group)) +
geom_bar(fill="steelblue") +
labs(title="Number of Patients per Group", x="Group", y="Count")- Histogram: Age distribution
ggplot(bp_data, aes(x=as.numeric(Age))) +
geom_histogram(binwidth=5, fill="lightgreen", color="black") +
labs(title="Age Distribution of Patients", x="Age", y="Frequency")- Scatterplot: Age vs BloodPressure, colored by Group
ggplot(bp_data, aes(x=Age, y=BloodPressure, color=Group)) +
geom_point() +
labs(title="Age vs Blood Pressure by Group",
x="Age", y="Blood Pressure")Bonus hands on
library(ggplot2)
library(patchwork) # install.packages("patchwork") if needed- Bar plot
p1 <- ggplot(bp_data, aes(x = Gender, y = BloodPressure, fill = Gender)) +
stat_summary(fun = "mean", geom = "bar") +
labs(title = "Average BP by Gender") +
theme_minimal()- Histogram
p2 <- ggplot(bp_data, aes(x=as.numeric(Age))) +
geom_histogram(binwidth=5, fill="lightgreen", color="black") +
labs(title="Age Distribution of Patients", x="Age", y="Frequency")- Boxplot
p3 <- ggplot(bp_data, aes(x = Group, y = BloodPressure, fill = Group)) +
geom_boxplot() +
labs(title = "BP by Group") +
theme_minimal()Combine plots into one figure
# horizontal layout
(p1 | p2 | p3)
# vertical layout
(p1 / p2 / p3)
# 2x2 grid
(p1 | p2) / p3